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- PDB-1iv2: Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1iv2 | ||||||
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Title | Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase (bound form CDP) | ||||||
![]() | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kishida, H. / Wada, T. / Unzai, S. / Kuzuyama, T. / Terada, T. / Sirouzu, M. / Yokoyama, S. / Tame, J.R.H. / Park, S.-Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Structure and catalytic mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis. Authors: Kishida, H. / Wada, T. / Unzai, S. / Kuzuyama, T. / Takagi, M. / Terada, T. / Shirouzu, M. / Yokoyama, S. / Tame, J.R. / Park, S.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 204.1 KB | Display | ![]() |
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PDB format | ![]() | 159.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1iv1C ![]() 1iv3C ![]() 1iv4C C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 16598.191 Da / Num. of mol.: 6 / Mutation: L41M, L81M, L120M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q8RQP5, ![]() #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CDP / ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.58 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 298 K / Method: evaporation / pH: 6.5 / Details: PEG, pH 6.5, EVAPORATION, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 5.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 20, 2001 / Details: mirrors |
Radiation | Monochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.55→20 Å / Num. all: 836026 / Num. obs: 118031 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.55→1.61 Å / Rmerge(I) obs: 0.248 / % possible all: 78.2 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 836026 |
Reflection shell | *PLUS % possible obs: 78.2 % |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Solvent model: MOEWS & KRETSINGER,J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 7606 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Num. reflection obs: 118031 / % reflection Rfree: 5.3 % / Rfactor all![]() ![]() ![]() | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_angle_d / Dev ideal: 0.026 |